Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,851,260	C→A	A115S (GCG→TCG)	acsA_1 ←	Acetyl‑coenzyme A synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,851,260	0	C	A	96.5%	97.1 / ‑2.4	29	coding (343/1707 nt)	acsA_1	Acetyl‑coenzyme A synthetase
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (11/17); minor base . (1/0); total (12/17)
Fisher's exact test for biased strand distribution p-value = 4.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

CTACAGGTACTCGAGGTAACAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGCAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGTATACGATTCTTTTCTGTGC  >  USA300TCH1516_ALE/1851116‑1851399

cTACAGGTACTCGAGGTAACAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGaaaa                                                                                                                                          <  4:139094/148‑1 (MQ=255)

cTACAGGTAATCGAGGTAACAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGaaaa                                                                                                                                          <  4:82892/148‑1 (MQ=255)

    aGGTACTCGAGGTAACAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAatat                                                                                                                                      >  3:23854/1‑148 (MQ=255)

                           tattaGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACataaa                                                                                                               <  3:231332/148‑1 (MQ=255)

                           tattaGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACataaa                                                                                                               <  3:52965/148‑1 (MQ=255)

                            attaGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAAGCGCCGTGTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGa                                                                                                                     <  1:1942/141‑1 (MQ=255)

                            attaGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACataaat                                                                                                              <  3:184700/148‑1 (MQ=255)

                            attaGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACataaat                                                                                                              <  3:387005/148‑1 (MQ=255)

                               aGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACataaatata                                                                                                           >  3:25265/1‑148 (MQ=255)

                                                             tAATCTATCCGCAACTGCCTTTTCCATAAATGTTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCa                                                                             >  4:398463/1‑148 (MQ=255)

                                                             tAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCa                                                                             >  4:336839/1‑148 (MQ=255)

                                                             tAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCa                                                                             >  4:414071/1‑148 (MQ=255)

                                                                tCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGt                                                                          >  3:402702/1‑148 (MQ=255)

                                                                 cTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACG‑AAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTc                                                                        >  3:277982/1‑148 (MQ=255)

                                                                               cTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTc                                                           >  3:353852/1‑148 (MQ=255)

                                                                                    ccATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGTCATAATTATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCgctgc                                                      <  3:95628/148‑1 (MQ=255)

                                                                                    ccATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCgctgc                                                      <  3:58300/148‑1 (MQ=255)

                                                                                        aaaTGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTtta                                                  >  3:340304/1‑148 (MQ=255)

                                                                                        aaaTGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTtta                                                  >  3:281589/1‑148 (MQ=255)

                                                                                           tGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTAAGGTGTACTCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATTTTCAGACAAAACATTCGCTGCTttattt                                               >  4:290412/1‑147 (MQ=255)

                                                                                                    tAACGTCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGt                                      <  4:162127/148‑1 (MQ=255)

                                                                                                    tAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCTACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGt                                      >  4:314261/1‑148 (MQ=255)

                                                                                                     aaCGGCCCAACAATTTCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGtt                                     <  4:165937/148‑1 (MQ=255)

                                                                                                                   tGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATaa                       <  3:414021/148‑1 (MQ=255)

                                                                                                                   tGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATaa                       <  3:196869/148‑1 (MQ=255)

                                                                                                                      aCCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGta                    <  3:43054/148‑1 (MQ=255)

                                                                                                                      aCCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGta                    <  3:48167/148‑1 (MQ=255)

                                                                                                                                  aaCACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGTATACGATTCtttt        <  4:297631/148‑1 (MQ=255)

                                                                                                                                  aaCACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGTATACGATTCtttt        <  3:30078/148‑1 (MQ=255)

                                                                                                                                    cacCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGTATACGATTCTTTTCt      <  3:130551/148‑1 (MQ=255)

                                                                                                                                        tAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGTATACGATTCTTTTCTGTGc  <  4:402702/148‑1 (MQ=255)

CTACAGGTACTCGAGGTAACAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGCAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGTATACGATTCTTTTCTGTGC  >  USA300TCH1516_ALE/1851116‑1851399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A